ExSRRF Analysis Code

In this repository you find the code used to register, evaluate and analyse the data in our publication. Please cite our publication when using our code:

Kylies, D., Zimmermann, M., Haas, F., Schwerk, M., Kuehl, M., Brehler, M., Czogalla, J., Hernandez, L. C., Konczalla, L., Okabayashi, Y., Menzel, J., Edenhofer, I., Mezher, S., Aypek, H., Dumoulin, B., Wu, H., Hofmann, S., Kretz, O., Wanner, N., Tomas, N. M., Krasemann, S., Glatzel, M., Kuppe, C., Kramann, R., Banjanin, B., Schneider, R. K., Urbschat, C., Arck, P., Gagliani, N., van Zandvoort, M., Wiech, T., Grahammer, F., Sáez, P. J., Wong, M. N., Bonn, S., Huber, T. B., Puelles, V. G. (2023). Expansion-enhanced super-resolution radial fluctuations enable nanoscale molecular profiling of pathology specimens. Nature Nanotechnology. doi:10.1038/s41565-023-01328-z.

register_time_stacks.py

Script that registers the time stacks saved as tiff files in a folder and calculated the SSIM and MSE to evaluate the registrations.

compare_exm_exsrrf_sted.ipynb

Notebook that was used to compare the SSIM between ridges and original images for ExM, ExSRRF and STED images.

ridges_slit_diaphragm.ipynb

Notebook to extract regions of interest and ridges (slit diaphragm) and calculate their densities

ridges_er_stress.ipynb

Notebook to extract regions of interest and ridges (ER) and calculate their densities

local_spacing.ipynb (GPLv3)

Notebook to compute the local spacing of ridge images. Local spacing calculation is based on the local_thickness plugin of Fiji (ImageJ) and was ported to python and adapted for our 2D use case.

Gallery

Output of local_spacing.ipynb for given sythetic test image:

1. original
2. distance transformed image
3. ridge image
4. local spacing image